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Hu X, Xia B, Ru W, Zhang Y, Yang J, Zhang H. Research progress on structure and catalytic mechanism of dextranase. EFOOD 2023. [DOI: 10.1002/efd2.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Xue‐Qin Hu
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Bing‐Bing Xia
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Wei‐Juan Ru
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Yu‐Xin Zhang
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Jing‐Wen Yang
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Hong‐Bin Zhang
- School of Food and Biological Engineering Hefei University of Technology Hefei China
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Dong D, Wang X, Deng T, Ning Z, Tian X, Zu H, Ding Y, Wang C, Wang S, Lyu M. A novel dextranase gene from the marine bacterium Bacillus aquimaris S5 and its expression and characteristics. FEMS Microbiol Lett 2021; 368:6105217. [PMID: 33476380 DOI: 10.1093/femsle/fnab007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/18/2021] [Indexed: 01/18/2023] Open
Abstract
Dextranase specifically hydrolyzes dextran and is used to produce functional isomalto-saccharide prebiotics. Moreover, dextranase is used as an additive in mouthwash to remove dental plaque. We cloned and expressed the dextranase gene of the marine bacterium Bacillus aquimaris S5. The length of the BaDex gene was 1788 bp, encoding 573 amino acids. Using bioinformatics to predict and analyze the amino acid sequence of BaDex, we found the isoelectric point and instability coefficient to be 4.55 and 29.22, respectively. The average hydrophilicity (GRAVY) was -0.662. The secondary structure of BaDex consisted of 145 alpha helices, accounting for 25.31% of the protein; 126 extended strands, accounting for 21.99%; and 282 random coils, accounting for 49.21%. The 3D structure of the BaDex protein was predicted and simulated using SWISS-MODEL, and BaDex was classified as a Glycoside Hydrolase Family 66 protein. The optimal temperature and pH for BaDex activity were 40°C and 6.0, respectively. The hydrolysates had excellent antioxidant activity, and 8 U/mL of BaDex could remove 80% of dental plaque in MBRC experiment. This recombinant protein thus has great promise for applications in the food and pharmaceutical industries.
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Affiliation(s)
- Dongxue Dong
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China
| | - Xuelian Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China
| | - Tian Deng
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China
| | - Zhe Ning
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China
| | - Xiaopeng Tian
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China
| | - Hangtian Zu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China
| | - Yanshuai Ding
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China
| | - Cang Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China.,Collaborative Innovation Center of Modern Biological Manufacturing, Anhui University, 111 Jiulong Road, Hefei 230039, China
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, 59 Cangwu Road, Lianyungang 222005, PR China.,Collaborative Innovation Center of Modern Biological Manufacturing, Anhui University, 111 Jiulong Road, Hefei 230039, China
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Liu H, Ren W, Ly M, Li H, Wang S. Characterization of an Alkaline GH49 Dextranase from Marine Bacterium Arthrobacter oxydans KQ11 and Its Application in the Preparation of Isomalto-Oligosaccharide. Mar Drugs 2019; 17:md17080479. [PMID: 31430863 PMCID: PMC6723167 DOI: 10.3390/md17080479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 11/16/2022] Open
Abstract
A GH49 dextranase gene DexKQ was cloned from marine bacteria Arthrobacter oxydans KQ11. It was recombinantly expressed using an Escherichia coli system. Recombinant DexKQ dextranase of 66 kDa exhibited the highest catalytic activity at pH 9.0 and 55 °C. kcat/Km of recombinant DexKQ at the optimum condition reached 3.03 s−1 μM−1, which was six times that of commercial dextranase (0.5 s−1 μM−1). DexKQ possessed a Km value of 67.99 µM against dextran T70 substrate with 70 kDa molecular weight. Thin-layer chromatography (TLC) analysis showed that main hydrolysis end products were isomalto-oligosaccharide (IMO) including isomaltotetraose, isomaltopantose, and isomaltohexaose. When compared with glucose, IMO could significantly improve growth of Bifidobacterium longum and Lactobacillus rhamnosus and inhibit growth of Escherichia coli and Staphylococcus aureus. This is the first report of dextranase from marine bacteria concerning recombinant expression and application in isomalto-oligosaccharide preparation.
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Affiliation(s)
- Hongfei Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Wei Ren
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- Collaborative Innovation Center of Modern Bio-Manufacture, Anhui University, Hefei 230039, China
| | - Mingsheng Ly
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Haifeng Li
- Medical College, Hangzhou Normal University, Hangzhou 311121, China.
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
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Suzuki N, Kishine N, Fujimoto Z, Sakurai M, Momma M, Ko JA, Nam SH, Kimura A, Kim YM. Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus. J Biochem 2015; 159:331-9. [PMID: 26494689 DOI: 10.1093/jb/mvv104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/12/2015] [Indexed: 11/12/2022] Open
Abstract
The crystal structures of the wild type and catalytic mutant Asp-312→Gly in complex with isomaltohexaose of endo-1,6-dextranase from the thermophilic bacterium Thermoanaerobacter pseudethanolicus (TpDex), belonging to the glycoside hydrolase family 66, were determined. TpDex consists of three structural domains, a catalytic domain comprising an (β/α)8-barrel and two β-domains located at both N- and C-terminal ends. The isomaltohexaose-complex structure demonstrated that the isomaltohexaose molecule was bound across the catalytic site, showing that TpDex had six subsites (-4 to +2) in the catalytic cleft. Marked movement of the Trp-376 side-chain along with loop 6, which was the side wall component of the cleft at subsite +1, was observed to occupy subsite +1, indicating that it might expel the cleaved aglycone subsite after the hydrolysis reaction. Structural comparison with other mesophilic enzymes indicated that several structural features of TpDex, loop deletion, salt bridge and surface-exposed charged residue, may contribute to thermostability.
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Affiliation(s)
- Nobuhiro Suzuki
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan;
| | - Naomi Kishine
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan;
| | - Zui Fujimoto
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan;
| | - Mutsumi Sakurai
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Mitsuru Momma
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Jin-A Ko
- Eco-Friendly Bio-material Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 580-185, Korea
| | - Seung-Hee Nam
- Department of Food Science and Technology and Functional Food Research Center, Chonnam National University, Gwangju 500-757, Korea
| | - Atsuo Kimura
- Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nisi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Young-Min Kim
- Department of Food Science and Technology and Functional Food Research Center, Chonnam National University, Gwangju 500-757, Korea; Bioenergy Research Center, Chonnam National University, Gwangju 500-757, Korea
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Abstract
The complete nucleotide sequence of the dextranase gene of Streptococcus rattus ATCC19645 was determined. An open reading frame of the dextranase gene was 2,760 bp long and encoded a dextranase protein consisting of 920 amino acids with a molecular weight of 100,163 Da and an isoelectric point of 4.67. The S. rattus dextranase purified from recombinant Escherichia coli cells showed dextran-hydrolyzing activity with optimal pH (5.0) and temperature (40 C) similar to those of dextranases from Streptococcus mutans and Streptococcus sobrinus. The deduced amino acid sequence of the S. rattus dextranase revealed that the dextranase molecule consists of two variable regions and a conserved region. The variable regions contained an N-terminal signal peptide and a C-terminal cell wall sorting signal; the conserved region contained two functional domains, catalytic and dextran-binding sites. This structural feature of the S. rattus dextranase is quite similar to that of other cariogenic species such as S. mutans, S. sobrinus, and Streptococcus downei.
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Affiliation(s)
- Takeshi Igarashi
- Department of Oral Microbiology, Showa University School of Dentistry, Tokyo, Japan.
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Kim YM, Yamamoto E, Kang MS, Nakai H, Saburi W, Okuyama M, Mori H, Funane K, Momma M, Fujimoto Z, Kobayashi M, Kim D, Kimura A. Bacteroides thetaiotaomicronVPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. FEBS J 2012; 279:3185-91. [DOI: 10.1111/j.1742-4658.2012.08698.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kim YM, Kiso Y, Muraki T, Kang MS, Nakai H, Saburi W, Lang W, Kang HK, Okuyama M, Mori H, Suzuki R, Funane K, Suzuki N, Momma M, Fujimoto Z, Oguma T, Kobayashi M, Kim D, Kimura A. Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. J Biol Chem 2012; 287:19927-35. [PMID: 22461618 PMCID: PMC3370177 DOI: 10.1074/jbc.m111.339036] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Revised: 03/27/2012] [Indexed: 11/06/2022] Open
Abstract
A novel endodextranase from Paenibacillus sp. (Paenibacillus sp. dextranase; PsDex) was found to mainly produce isomaltotetraose and small amounts of cycloisomaltooligosaccharides (CIs) with a degree of polymerization of 7-14 from dextran. The 1,696-amino acid sequence belonging to the glycosyl hydrolase family 66 (GH-66) has a long insertion (632 residues; Thr(451)-Val(1082)), a portion of which shares identity (35% at Ala(39)-Ser(1304) of PsDex) with Pro(32)-Ala(755) of CI glucanotransferase (CITase), a GH-66 enzyme that catalyzes the formation of CIs from dextran. This homologous sequence (Val(837)-Met(932) for PsDex and Tyr(404)-Tyr(492) for CITase), similar to carbohydrate-binding module 35, was not found in other endodextranases (Dexs) devoid of CITase activity. These results support the classification of GH-66 enzymes into three types: (i) Dex showing only dextranolytic activity, (ii) Dex catalyzing hydrolysis with low cyclization activity, and (iii) CITase showing CI-forming activity with low dextranolytic activity. The fact that a C-terminal truncated enzyme (having Ala(39)-Ser(1304)) has 50% wild-type PsDex activity indicates that the C-terminal 392 residues are not involved in hydrolysis. GH-66 enzymes possess four conserved acidic residues (Asp(189), Asp(340), Glu(412), and Asp(1254) of PsDex) of catalytic candidates. Their amide mutants decreased activity (1⁄1,500 to 1⁄40,000 times), and D1254N had 36% activity. A chemical rescue approach was applied to D189A, D340G, and E412Q using α-isomaltotetraosyl fluoride with NaN(3). D340G or E412Q formed a β- or α-isomaltotetraosyl azide, respectively, strongly indicating Asp(340) and Glu(412) as a nucleophile and acid/base catalyst, respectively. Interestingly, D189A synthesized small sized dextran from α-isomaltotetraosyl fluoride in the presence of NaN(3).
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Affiliation(s)
- Young-Min Kim
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yoshiaki Kiso
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Tomoe Muraki
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Min-Sun Kang
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Hiroyuki Nakai
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Wataru Saburi
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Weeranuch Lang
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Hee-Kwon Kang
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Masayuki Okuyama
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Haruhide Mori
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Ryuichiro Suzuki
- the National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642, Japan
| | - Kazumi Funane
- the National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642, Japan
| | - Nobuhiro Suzuki
- the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Mitsuru Momma
- the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Zui Fujimoto
- the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Tetsuya Oguma
- the Noda Institute for Scientific Research, 399 Noda, Noda 278-0037, Japan
| | - Mikihiko Kobayashi
- the Department of Food and Health Science, Jissenn Women's University, Hino 191-8510, Japan, and
| | - Doman Kim
- the School of Biological Sciences and Technology, Chonnam National University, Gwangju 500-757, Korea
| | - Atsuo Kimura
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K, Kimura A. Structural elucidation of dextran degradation mechanism by streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem 2012; 287:19916-26. [PMID: 22337884 DOI: 10.1074/jbc.m112.342444] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dextranase is an enzyme that hydrolyzes dextran α-1,6 linkages. Streptococcus mutans dextranase belongs to glycoside hydrolase family 66, producing isomaltooligosaccharides of various sizes and consisting of at least five amino acid sequence regions. The crystal structure of the conserved fragment from Gln(100) to Ile(732) of S. mutans dextranase, devoid of its N- and C-terminal variable regions, was determined at 1.6 Å resolution and found to contain three structural domains. Domain N possessed an immunoglobulin-like β-sandwich fold; domain A contained the enzyme's catalytic module, comprising a (β/α)(8)-barrel; and domain C formed a β-sandwich structure containing two Greek key motifs. Two ligand complex structures were also determined, and, in the enzyme-isomaltotriose complex structure, the bound isomaltooligosaccharide with four glucose moieties was observed in the catalytic glycone cleft and considered to be the transglycosylation product of the enzyme, indicating the presence of four subsites, -4 to -1, in the catalytic cleft. The complexed structure with 4',5'-epoxypentyl-α-d-glucopyranoside, a suicide substrate of the enzyme, revealed that the epoxide ring reacted to form a covalent bond with the Asp(385) side chain. These structures collectively indicated that Asp(385) was the catalytic nucleophile and that Glu(453) was the acid/base of the double displacement mechanism, in which the enzyme showed a retaining catalytic character. This is the first structural report for the enzyme belonging to glycoside hydrolase family 66, elucidating the enzyme's catalytic machinery.
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Affiliation(s)
- Nobuhiro Suzuki
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
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Suzuki N, Kim YM, Fujimoto Z, Momma M, Kang HK, Funane K, Okuyama M, Mori H, Kimura A. Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1542-4. [PMID: 22139161 PMCID: PMC3232134 DOI: 10.1107/s1744309111038425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 09/19/2011] [Indexed: 11/10/2022]
Abstract
Streptococcus mutans dextranase hydrolyzes the internal α-1,6-linkages of dextran and belongs to glycoside hydrolase family 66. An N- and C-terminal deletion mutant of S. mutans dextranase was crystallized by the sitting-drop vapour-diffusion method. The crystals diffracted to a resolution of 1.6 Å and belonged to space group P2(1), with unit-cell parameters a = 53.2, b = 89.7, c = 63.3 Å, β = 102.3°. Assuming that the asymmetric unit of the crystal contained one molecule, the Matthews coefficient was calculated to be 4.07 Å(3) Da(-1); assuming the presence of two molecules in the asymmetric unit it was calculated to be 2.03 Å(3) Da(-1).
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Affiliation(s)
- Nobuhiro Suzuki
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Young-Min Kim
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Zui Fujimoto
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Mitsuru Momma
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hee-Kwon Kang
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Kazumi Funane
- Applied Microbiology Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba 305-8642, Japan
| | - Masayuki Okuyama
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Atsuo Kimura
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
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Truncation of N- and C-terminal regions of Streptococcus mutans dextranase enhances catalytic activity. Appl Microbiol Biotechnol 2011; 91:329-39. [DOI: 10.1007/s00253-011-3201-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 02/16/2011] [Accepted: 02/18/2011] [Indexed: 10/18/2022]
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Dextran glucosidase: A potential target of iminosugars in caries prevention. Med Hypotheses 2011; 76:574-5. [DOI: 10.1016/j.mehy.2011.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 11/10/2010] [Accepted: 01/05/2011] [Indexed: 11/27/2022]
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Maruyama F, Kobata M, Kurokawa K, Nishida K, Sakurai A, Nakano K, Nomura R, Kawabata S, Ooshima T, Nakai K, Hattori M, Hamada S, Nakagawa I. Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content. BMC Genomics 2009; 10:358. [PMID: 19656368 PMCID: PMC2907686 DOI: 10.1186/1471-2164-10-358] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 08/05/2009] [Indexed: 11/20/2022] Open
Abstract
Background Streptococcus mutans is the major pathogen of dental caries, and it occasionally causes infective endocarditis. While the pathogenicity of this species is distinct from other human pathogenic streptococci, the species-specific evolution of the genus Streptococcus and its genomic diversity are poorly understood. Results We have sequenced the complete genome of S. mutans serotype c strain NN2025, and compared it with the genome of UA159. The NN2025 genome is composed of 2,013,587 bp, and the two strains show highly conserved core-genome. However, comparison of the two S. mutans strains showed a large genomic inversion across the replication axis producing an X-shaped symmetrical DNA dot plot. This phenomenon was also observed between other streptococcal species, indicating that streptococcal genetic rearrangements across the replication axis play an important role in Streptococcus genetic shuffling. We further confirmed the genomic diversity among 95 clinical isolates using long-PCR analysis. Genomic diversity in S. mutans appears to occur frequently between insertion sequence (IS) elements and transposons, and these diversity regions consist of restriction/modification systems, antimicrobial peptide synthesis systems, and transporters. S. mutans may preferentially reject the phage infection by clustered regularly interspaced short palindromic repeats (CRISPRs). In particular, the CRISPR-2 region, which is highly divergent between strains, in NN2025 has long repeated spacer sequences corresponding to the streptococcal phage genome. Conclusion These observations suggest that S. mutans strains evolve through chromosomal shuffling and that phage infection is not needed for gene acquisition. In contrast, S. pyogenes tolerates phage infection for acquisition of virulence determinants for niche adaptation.
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Affiliation(s)
- Fumito Maruyama
- Division of Bacteriology, Department of Infectious Diseases Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.
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Kim YM, Kim D. Characterization of novel thermostable dextranase from Thermotoga lettingae TMO. Appl Microbiol Biotechnol 2009; 85:581-7. [DOI: 10.1007/s00253-009-2121-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 06/29/2009] [Accepted: 06/30/2009] [Indexed: 11/28/2022]
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Khalikova E, Susi P, Korpela T. Microbial dextran-hydrolyzing enzymes: fundamentals and applications. Microbiol Mol Biol Rev 2005; 69:306-25. [PMID: 15944458 PMCID: PMC1197420 DOI: 10.1128/mmbr.69.2.306-325.2005] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Dextran is a chemically and physically complex polymer, breakdown of which is carried out by a variety of endo- and exodextranases. Enzymes in many groups can be classified as dextranases according to function: such enzymes include dextranhydrolases, glucodextranases, exoisomaltohydrolases, exoisomaltotriohydrases, and branched-dextran exo-1,2-alpha-glucosidases. Cycloisomalto-oligosaccharide glucanotransferase does not formally belong to the dextranases even though its side reaction produces hydrolyzed dextrans. A new classification system for glycosylhydrolases and glycosyltransferases, which is based on amino acid sequence similarities, divides the dextranases into five families. However, this classification is still incomplete since sequence information is missing for many of the enzymes that have been biochemically characterized as dextranases. Dextran-degrading enzymes have been isolated from a wide range of microorganisms. The major characteristics of these enzymes, the methods for analyzing their activities and biological roles, analysis of primary sequence data, and three-dimensional structures of dextranases have been dealt with in this review. Dextranases are promising for future use in various scientific and biotechnological applications.
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Affiliation(s)
- Elvira Khalikova
- Joint Biotechnology Laboratory, Department of Chemistry, University of Turku, Finland
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Igarashi T, Asaga E, Goto N. Roles of Streptococcus mutans dextranase anchored to the cell wall by sortase. ACTA ACUST UNITED AC 2004; 19:102-5. [PMID: 14871349 DOI: 10.1046/j.0902-0055.2003.00123.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In order to clarify the role that sortase (SrtA) plays in anchoring dextranase (Dex) to the cell wall of Streptococcus mutans, both Dex- and SrtA- mutants were constructed by insertional inactivation of the respective genes. Western blot analysis with a Dex antiserum showed that in the srtA mutant the Dex was not bound to the cell wall but was secreted into the culture supernatant. In contrast, in the wild type, Dex remained cell-wall-associated. Biological properties of the srtA mutant were examined in dextran fermentation, colony morphology and adherence to a smooth surface. The srtA mutant, as well as the wild type, retained the ability to ferment dextran. However, the colony morphology of the srtA mutant on Todd Hewitt agar containing sucrose was much larger than that of the wild type and showed a ring-like structure. In addition, the srtA mutant was more adhesive to a smooth surface than the wild type when sucrose was present. However, the adhesion of the srtA mutant remarkably decreased by addition of exogenous dextranase. These studies suggest that the SrtA mediates Dex-anchoring to the cell wall in S. mutans, and cell wall-anchored Dex plays a role in controlling both the adhesive properties of extracellular glucan and the ability to utilize extracellular glucan as a nutrient source. In contrast, extracellular Dex is only responsible for degrading extracellular glucan as a nutrient source.
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Affiliation(s)
- T Igarashi
- Department of Oral Microbiology, Showa University School of Dentistry, Tokyo, Japan.
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Khalikova E, Susi P, Usanov N, Korpela T. Purification and properties of extracellular dextranase from a Bacillus sp. J Chromatogr B Analyt Technol Biomed Life Sci 2003; 796:315-26. [PMID: 14581071 DOI: 10.1016/j.jchromb.2003.08.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Bacterial strains in the genus Bacillus were isolated from natural soil samples and screened for production of extracellular dextranases (E.C.3.2.1.11). One strain, determined by 16sRNA analysis as Paenibacillus illinoisensis exhibiting stable dextranase activity, was chosen for further analysis, and the dextranase from it was purified 733-fold using salt and PEG precipitations, two-phase extraction and DEAE-Sepharose chromatography with a total yield of 19%. The purified enzyme had three isoforms, with molecular masses of 76, 89 and 110kDa and isoelectric points of 4.95, 4.2 and 4.0, respectively. The mixture of the three dextranase isoforms has a broad pH optimum around pH 6.8 and a temperature optimum at 50 degrees C. The N-terminal sequence (Ala-Ser-Thr-Gly-Lys) was identical between the isoforms. No sequence homology with the known dextranases in the protein databanks was found.
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Affiliation(s)
- Elvira Khalikova
- Joint Biotechnology Laboratory, University of Turku, BioCity 6A, FIN-20520 Turku, Finland
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Igarashi T, Morisaki H, Yamamoto A, Goto N. An essential amino acid residue for catalytic activity of the dextranase of Streptococcus mutans. ORAL MICROBIOLOGY AND IMMUNOLOGY 2002; 17:193-6. [PMID: 12030973 DOI: 10.1034/j.1399-302x.2002.170310.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Dextranase (Dex) is an enzyme that hydrolyzes glucan, a polymer of glucose synthesized from sucrose by glucosyltransferases (GTFs). By comparing amino acid sequences of Dexs and GTFs, we found that the Dex enzymes of Streptococcus mutans, Streptococcus sobrinus, Streptococcus downei and Streptococcus salivarius had similar amino acid sequences to those of the catalytic sites of GTFs of mutans streptococci. We therefore examined the amino acid essential in Dex catalysis by molecular genetic approaches in this study. Site-directed mutagenesis was used to convert the Asp-385 of the Dex molecule of S. mutans Ingbritt to Glu, Asn, Thr or Val. Replacement of Asp-385 with any of the amino acids resulted in complete disappearance of Dex activity. However, replacement of other Asp residues did not affect the enzyme activity. The inactive enzymes still retained dextran-binding ability. These results suggest that Asp-385 of the Dex of S. mutans Ingbritt was essential for enzyme activity and the catalytic and substrate-binding sites were located at different sites within the Dex molecule.
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Affiliation(s)
- T Igarashi
- Department of Oral Microbiology, Showa University School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
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Igarashi T, Yamamoto A, Goto N. Nucleotide sequence and molecular characterization of a dextranase gene from Streptococcus downei. Microbiol Immunol 2002; 45:341-8. [PMID: 11471821 DOI: 10.1111/j.1348-0421.2001.tb02629.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA fragments encoding the Streptococcus downei dextranase were amplified by PCR and inverse PCR based on a comparison of the dextranase gene (dex) sequences from S. sobrinus, S. mutans, and S. salivarius, and the complete nucleotide sequence of the S. downei dex was determined. An open reading frame (ORF) of dex was 3,891 bp long. It encoded a dextranase protein (Dex) consisting of 1,297 amino acids with a molecular mass of 139,743 Da and an isoelectric point of 4.49. The deduced amino acid sequence of S. downei Dex had homology to those of S. sobrinus, S. mutans and S. salivanus Dex in the conserved region (made of about 540 amino acid residues). DNA hybridization analysis showed that a dex DNA probe of S. downei hybridized to the chromosomal DNA of S. sobrinus as well as that of S. downei, but did not to other species of mutans streptococci. The C terminus of the S. downei Dex had a membrane-anchor region which has been reported as a common structure of C termini of both the S. mutans and S. sobrinus Dex. The recombinant plasmid which harbored the dex ORF of S. downei produced a recombinant Dex enzyme in Escherichia coli cells. The analysis of the recombinant enzyme on SDS-PAGE containing blue dextran showed multiple active forms as well as dextranases of S. mutans, S. sobrinus and S. salivarius.
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Affiliation(s)
- T Igarashi
- Department of Oral Microbiology, Showa University School of Dentistry, Tokyo, Japan.
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Igarashi T, Yano Y, Yamamoto A, Sasa R, Goto N. Identification of Streptococcus salivarius by PCR and DNA probe. Lett Appl Microbiol 2001; 32:394-7. [PMID: 11412350 DOI: 10.1046/j.1472-765x.2001.00928.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To establish species-specific PCR and DNA probe methods for Streptococcus salivarius and to clarify the distribution of dextranase in oral isolates of Strep. salivarius. METHODS AND RESULTS A pair of PCR primers and a DNA probe were designed based on the nucleotide sequence of the dextranase gene of Strep. salivarius JCM5707. Both the PCR primer and the DNA probe specifically detected Strep. salivarius but none of the other oral streptococci (23 strains of 13 species). The primer and the probe were capable of detecting 1 pg and 1 ng of the genomic DNA, respectively, purified from Strep. salivarius JCM5707. All oral isolates (130 strains from 12 subjects) of Strep. salivarius from human saliva were positive by both methods. CONCLUSION The present PCR and DNA probe methods are highly specific to Strep. salivarius and are useful for the its detection and identification of this bacterium. The dextranase widely distributes among oral isolates of Strep. salivarius. SIGNIFICANCE AND IMPACT OF THE STUDY The DNA sequence of a dextranase gene present in the genome of Strep. salivarius is useful as the target DNA of the species-specific PCR and DNA probe.
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Affiliation(s)
- T Igarashi
- Department of Oral Microbiology, Showa University School of Dentistry, Tokyo, Japan.
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Igarashi T, Yamamoto A, Goto N. Detection of dextranase-producing gram-negative oral bacteria. ORAL MICROBIOLOGY AND IMMUNOLOGY 1998; 13:382-6. [PMID: 9872116 DOI: 10.1111/j.1399-302x.1998.tb00696.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thirty-one strains of 23 gram-negative oral bacterial species were examined for dextran-degrading activity on agar plates containing blue dextran. One strain each of Capnocytophaga ochracea, Capnocytophaga sputigena, Prevotella loescheii, Prevotella melaninogenica and Prevotella oralis had detectable dextranase activity. The culture supernatants of P. melaninogenica and P. oralis cells contained dextranases of multiple sizes, but those of the other three species had a single size of enzyme. A 56-kDa dextranase was purified from the culture supernatant of P. oralis and the antiserum against the enzyme was prepared with a rabbit. The Ouchterlony test showed that the antibody reacted with the supernatants of both P. melaninogenica and P. oralis but not with the others. Dot-blot hybridization using the dextranase gene of Streptococcus mutans as a probe revealed that there was no significantly homologous sequence in the chromosomal DNA of the five species.
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Affiliation(s)
- T Igarashi
- Department of Oral Microbiology, Showa University School of Dentistry, Tokyo, Japan
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Abstract
Mutans streptococci are considered the predominant pathogens in dental caries. Three methods, i.e. dot blot hybridization analysis, PCR analysis and SDS-blue dextran-PAGE, were examined for identifying mutans streptococcal species. In dot blot hybridization, DNA probe derived from the dextranse gene (dexA) of Streptococcus mutans hybridized with different intensities under the condition of low stringency against each species of mutans streptococci although the dexA probe was specific for S. mutans under the condition of high stringency. Oligonucleotide primers for polymerase chain reaction (PCR) were designed on the basis of the dexA DNA sequence. The primers amplified species-specific PCR products in the reference species (15 strains of 5 species) of mutants streptococci. An electrophoretic profile of dextranases from the mutans streptococci on SDS-blue dextran-PAGE also showed species-specific behavior. These results suggest that the three identification methods examined here are useful for distinguishing the species of mutans streptococci and also indicate that PCR analysis is suitable for simple, rapid and reliable identification of mutans streptococcal species.
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Affiliation(s)
- T Igarashi
- Department of Oral Microbiology, Showa University School of Dentistry, Tokyo, Japan
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Igarashi T, Yamamoto A, Goto N. Direct detection of Streptococcus mutans in human dental plaque by polymerase chain reaction. ORAL MICROBIOLOGY AND IMMUNOLOGY 1996; 11:294-8. [PMID: 9028253 DOI: 10.1111/j.1399-302x.1996.tb00184.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Streptococcus mutans is an etiological agent in human dental caries. A method for the detection of S. mutans directly from human dental plaque by polymerase chain reaction has been developed. Oligonucleotide primers specific for a portion of the dextranase gene (dexA) of S. mutans Ingbritt (serotype c) were designed to amplify a 1272-bp DNA fragment by polymerase chain reaction. The present method specifically detected S. mutans (serotypes c, e and f), but none of the other mutans streptococci: S. cricetus (serotype a), S. rattus (serotype b), S. sobrinus (serotypes d and g), and S. downei (serotype h), other gram-positive bacteria (16 strains of 12 species of cocci and 18 strains of 12 species of bacilli) nor gram-negative bacteria (1 strain of 1 species of cocci and 20 strains of 18 species of bacilli). The method was capable of detecting 1 pg of the chromosomal DNA purified from S. mutans Ingbritt and as few as 12 colony-forming units of S. mutans cells. The S. mutans cells in human dental plaque were also directly detected. Seventy clinical isolates of S. mutans isolated from the dental plaque of 8 patients were all positive by the polymerase chain reaction. These results suggest that the dexA polymerase chain reaction is suitable for the specific detection and identification of S. mutans.
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Affiliation(s)
- T Igarashi
- Department of Oral Microbiology, Showa University School of Dentistry, Tokyo, Japan
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Igarashi T, Yamamoto A, Goto N. Sequence analysis of the Streptococcus mutans Ingbritt dexA gene encoding extracellular dextranase. Microbiol Immunol 1995; 39:853-60. [PMID: 8657012 DOI: 10.1111/j.1348-0421.1995.tb03282.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The complete nucleotide sequence (3,747 bp) of the dextranase gene (dexA) and flanking regions of the chromosome of Streptococcus mutans Ingbritt (serotype c) were determined. The open reading frame for dexA was 2,550 bp, ending with a stop codon TGA. A putative ribosome-binding site, promoter preceding the start codon, and potential stem-loop structure were identified. The presumed dextranase protein (DexA) consisting of 850 amino acids was estimated to have a molecular size of 94,536 Da and a pI of 4.79. The nucleotide sequence and the deduced amino acid sequences of S. mutans dexA exhibited homologies of 57.8% and 47.0%, respectively, to those of Streptococcus sobrinus dex. The homologous region of dex of S. sobrinus was in the N-terminal half. The C terminus of DexA consisted of a hexapeptide LPQTGD, followed by 7 charged amino acids, 21 amino acids with a strongly hydrophobic character, and a charged hexapeptide tail, which have been reported as a common structure of C termini of not only the surface-associated proteins of Gram-positive cocci but also the extracellular enzymes such as beta-fructosidase of S. mutans and dextranase of S. sobrinus. The DexA protein had no significant homology with the glucosyltransferases, the glucan-binding protein, or the dextranase inhibitor of mutans streptococci.
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Affiliation(s)
- T Igarashi
- Department of Oral Microbiology, Showa University School of Dentistry, Tokyo, Japan
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